Search for Variation information by Variation ID:
Detailed information for vg0209814096:
| Variant ID: vg0209814096 (JBrowse) | Variation Type: SNP |
| Chromosome: chr02 | Position: 9814096 |
| Reference Allele: T | Alternative Allele: C |
| Primary Allele: T | Secondary Allele: C |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
AGACCTCTTGCATTGCAGACATCGCGACGGATGAATCGGTAGAGGTCAGTGGCCACGTTCAAGATAAGTGGCCACGTTCAAGATAGTAGTGTCGTTGAAT[T/C]
GTTGTGCAATATATGGGATTTCGGGGATCTGCGCACAAAAAGGAAAATAAAATGGTACTCAGTGAGAAGTGTGTGCGAGATGGGTTTCTTTGTAGAGAAG
Reverse complement sequence
CTTCTCTACAAAGAAACCCATCTCGCACACACTTCTCACTGAGTACCATTTTATTTTCCTTTTTGTGCGCAGATCCCCGAAATCCCATATATTGCACAAC[A/G]
ATTCAACGACACTACTATCTTGAACGTGGCCACTTATCTTGAACGTGGCCACTGACCTCTACCGATTCATCCGTCGCGATGTCTGCAATGCAAGAGGTCT
Allele Frequencies:
| Populations | Population Size | Frequency of T(primary allele) | Frequency of C(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 72.20% | 0.30% | 2.64% | 24.84% | NA |
| All Indica | 2759 | 63.20% | 0.20% | 1.59% | 34.98% | NA |
| All Japonica | 1512 | 93.10% | 0.20% | 4.10% | 2.65% | NA |
| Aus | 269 | 40.10% | 1.90% | 4.46% | 53.53% | NA |
| Indica I | 595 | 64.20% | 0.00% | 2.02% | 33.78% | NA |
| Indica II | 465 | 53.50% | 0.60% | 2.37% | 43.44% | NA |
| Indica III | 913 | 68.20% | 0.10% | 0.99% | 30.67% | NA |
| Indica Intermediate | 786 | 62.50% | 0.10% | 1.53% | 35.88% | NA |
| Temperate Japonica | 767 | 94.90% | 0.40% | 3.00% | 1.69% | NA |
| Tropical Japonica | 504 | 91.50% | 0.00% | 4.37% | 4.17% | NA |
| Japonica Intermediate | 241 | 90.50% | 0.00% | 7.05% | 2.49% | NA |
| VI/Aromatic | 96 | 84.40% | 1.00% | 2.08% | 12.50% | NA |
| Intermediate | 90 | 78.90% | 1.10% | 5.56% | 14.44% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0209814096 | T -> DEL | LOC_Os02g17140.1 | N | frameshift_variant | Average:22.447; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | N | N | N | N |
| vg0209814096 | T -> C | LOC_Os02g17140.1 | missense_variant ; p.Gln1328Arg; MODERATE | nonsynonymous_codon ; Q1328R | Average:22.447; most accessible tissue: Zhenshan97 flag leaf, score: 44.637 | possibly damaging  |
-1.549 |
TOLERATED | 1.00 |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0209814096 | 1.73E-07 | 1.73E-07 | mr1954_2 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |